The theme of this research is that T cells vary in their specificity of recognition of a complex of class II MHC molecules with a given peptide. This variation in specificity is dictated by the processing/peptide loading events. The seminal issue here is that this difference in specificity influences the selection of T cells in the thymus to an autologous peptide and could influence autoimmunity. When lysozyme (HEL) is offered to APC and processed it results in the generation of a family of peptides comprising the core sequence 52-60 and variable flanking residues usually from 48-63. T cells generated against HEL are referred to as type A. When peptides with the same sequence as the processed peptides are offered to the APC, a distinct set of T cells are generated that recognize only the exogenous peptide and not the processed HEL. (Exogenous peptide can also stimulate type A T cells.) We also found that while HEL transgenic mice are completely tolerant to HEL, immunization with the peptide shows that many type B set escapes negative selection. We propose analyzing a large range of T cells and testing them against peptides that have changes in their MHC anchor and TCR contact amino acids. Initial data indicates that the recognition of the TCR contact residues by type B may be different from the type A. We propose solving the biochemical basis of the peptide-MHC complex that give rise to the distinct T cells; it includes making monoclonal antibodies to the various complexes of peptide and MHC producing the complexes with baculovirus purified I-Ak molecules under a number of conditions including in the absence or presence of H-2DM; and resolving their structure by x-ray crystallography. We propose experiments on APC to determine how type B complexes can be generated from either intracellular handling of the protein or by extracellular proteolysis. We include analysis of the peptide by mass spectrometry. Finally, the significance of the type B is explored by the production of TCR transgenic mice of two representative type B clones and determining the life history of the T cells under conditions where HEL is also expressed in tissues. We consider whether such clones directed to type B complexes can contribute to autoimmunity to HEL under inflammatory conditions where the protein may be partially proteolyzed. We present experiments exploring their role in bacterial immunity.